<tool profile="16.07" id="mothur_get_otulabels" name="Get.otulabels" version="@WRAPPER_VERSION@.0">
    <description>Selects OTU labels</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$infile.otu' infile.otu.dat &&
ln -s '$accnos' accnos.dat &&

echo 'get.otulabels(
    #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
        constaxonomy=infile.otu.dat,
    #end if
    #if $infile.otu.is_of_type("mothur.otu.corr"):
        otucorr=infile.otu.dat,
    #end if
    #if $infile.otu.is_of_type("mothur.axes"):
        corraxes=infile.otu.dat,
    #end if
    #if $infile.otu.is_of_type("mothur.list"):
        list=infile.otu.dat,
    #end if
    #if $infile.otu.is_of_type("mothur.shared"):
        shared=infile.otu.dat,
    #end if
    #if $infile.intype == "in_shared" and $infile.label:
        label=$infile.label,
    #end if
    accnos=accnos.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
        <conditional name="infile">
            <param name="intype" type="select" label="Which type of files will you be supplying?" help="">
                <option value="in_shared">Shared or List file</option>
                <option value="in_other">Constaxonomy / OtuCorr / CorrAxes file</option>
            </param>
            <when value="in_shared">
                <param name="otu" type="data" format="mothur.list,mothur.shared" label="shared/list - allows you to input a list file you wish to select OTUs from. "/>
                <param name="label" type="select" label="label - pick (one) OTU Label" optional="true" help="By default first label in your file is used">
                    <expand macro="labeloptions"/>
                </param>
            </when>
            <when value="in_other">
                <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/>
            </when>
        </conditional>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/>
    </outputs>
    <tests>
        <test>
            <param name="intype" value="in_shared"/>
            <param name="accnos" value="amazon.accnos.otulabels"/>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="label" value="0.22"/>
            <output name="pick_out" md5="1868b58c69f48fe0ae14113d1fc50b33" ftype="mothur.shared"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="intype" value="in_other"/>
            <param name="accnos" value="amazon.accnos.otulabels"/>
            <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
            <output name="pick_out" md5="c5f9d1a80b85cce640f25eb89cb67509" ftype="mothur.axes"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@


**Command Documentation**

The get.otulabels command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected.

.. _classify.otu: https://www.mothur.org/wiki/Classify.otu
.. _corr.axes: https://www.mothur.org/wiki/Corr.axes
.. _otu.association: https://www.mothur.org/wiki/Otu.association

v.1.27.0: Added list and shared parameters, updated to Mothur 1.33

    ]]></help>
    <expand macro="citations"/>
</tool>